Mitoz is not working in different directory

[asifratul]

MitoZ version?

3.4

How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code)

conda-pack (cannot dockers are showing some issues)

Did you run a test after your installation, and was the test run okay?

yes. I make a test folder inside the home directory.
and it worked well. when I mount in another directory, the test dataset is not working.

The command you used?

source ~/mitoz3.4/bin/activate
cd /mnt/e/AsifAnalysis/mitoZ/test
mitoz all --fq1 test.1.fq.gz --fq2 test.2.fq.gz --outprefix ttt --clade Arthropoda --data_size_for_mt_assembly 0 --assembler megahit --requiring_taxa Arthropoda

Problem description

HI,

I am getting problem frequently. I install the conda-pack, as the dockers are not being installed in my ubuntu 18.02.5 (installed on windows). When I first ran the soft for test data, it work well in home directory. But when I change the directory to separate folder, it is giving errors.

I assume, there might be issues in different directory.
I then copy my fastq files in the test folder in home directory, but it is also giving same errors.
can you please let me know, what can I do?

Log messages from MitoZ (stdout and stderr)

mitoz.log

[asifratul]

Seeming, spades assembler is working! anyway to fix the megahit issue?

mitoz.log

[linzhi2013]

Hi Asifratul,

About the Megahit, can you excute the command within the enviroment?

megahit  --out-dir ./megahit_out  --num-cpu-threads 8 --k-list 21,29,39,59,79,99,119,141 --memory 500000000000.0 -1 /mnt/e/AsifAnalysis/mitoZ/test/clean_data/ttt.clean_R1.fq.gz -2 /mnt/e/AsifAnalysis/mitoZ/test/clean_data/ttt.clean_R2.fq.gz  >megahit.log 2>megahit.err

and see what is in megahit.log and megahit.err.

[asifratul]

Getting the same errors!

megahit.err.txt

[linzhi2013]

Getting the same errors!

megahit.err.txt

thanks!

Seems to be related to your file system. Similar problems have been raised on nmquijada/tormes#21 and voutcn/megahit#303 and https://groups.google.com/g/3d-genomics/c/UQLyV2nDISQ

On the third link, they suggest

It's possible that your environment is configured to use a different temp directory instead of "/tmp" so try to find it using "env |grep -i tmp" command. If you see an environment variable defined like TMPDIR (or something similar) then use "--tmp-dir $TMPDIR" instead of "--tmp-dir /tmp"

[asifratul]

Hi @linzhi2013,

adding "--tmp-dir /tmp" within the maghit command works perfectly! Many thanks, much appreciated.
Is there any way to add this temp directory command within "mitoz all" command ?

ASIF

[linzhi2013]

Hi ASIF,

that's great.

You can find the megahit commands in the assembly.py file:

    if resume:
        command = "megahit --continue --out-dir ./megahit_out "
        runcmd(command, logger=logger)
    else:
        if fq1 and fq2:
            command = "megahit " +\
                " --out-dir ./megahit_out "+\
                " --num-cpu-threads " + thread_number +\
                " --k-list " + kmers +\
                " --memory " + str(memory) +\
                " -1 " + fq1 +\
                " -2 " + fq2
        else:
            command = "megahit " +\
                " --out-dir ./megahit_out " +\
                " --num-cpu-threads " + thread_number +\
                " --k-list " + kmers +\
                " --memory " + str(memory) +\
                " --read " + fq1
        runcmd(command, logger=logger)

And then add --tmp-dir ./megahit_tmp to the above megahit commands.

Or

use --tmp-dir $TMPDIR, but define the $TMPDIR variable before using the mitoz command, like:

export TMPDIR=/some/dir/ && mitoz all XXXXX

[linzhi2013]

I will incorporate such an option into MitoZ in subsequent releases. thanks again for your reporting!

[asifratul]

Hi @linzhi2013 ,

Thanks for the code. I have incorporated your codes in assembly.py. but still, it is giving the same error!

[linzhi2013]

I see. Maybe you have used the wrong way because the google group says defined like TMPDIR (or something similar) then use "--tmp-dir $TMPDIR" instead of --tmp-dir /tmp". See my updated answer.

[asifratul]

Hi @linzhi2013,

I might not get your suggestion properly. what I have done is -

a. added your megahit codes in assembly.py file, with --temp-dir $TMPDIR (see below).
b. then run --> export TMPDIR=./megatemp && mitoz all --fq1 test.1.fq.gz --fq2 test.2.fq.gz --outprefix ttt --clade Arthropoda --data_size_for_mt_assembly 0 --assembler megahit --requiring_taxa Arthropoda

but still getting the same error! Am I doing something wrong?

ASIF

mitoz.log

[linzhi2013]

I don't know if you have to create the TMPDIR directory before using it (I suppose you need to).

The another thing I am not so sure is if the TMPDIR variable can be passed to the megahit command with MitoZ using the above method.

I would suggest not use the TMPDIR variable method, but using thehard-code way:

Firstly, create the path of a tmp directory:

mkdir -p /your/custom/tmp/path

Then replace the --tmp-dir $TMPDIR in the assembly.py file with --tmp-dir /your/custom/tmp/path.

Also don't forget to do the same thing with

[linzhi2013]

See https://github.com/linzhi2013/MitoZ/releases/tag/3.5